Posted: 24 Sep 2008 06:10 PM CDT
Okay, we don’t get it. Google Trend searches of terms like GMO, DNA, Transgenic and Biotechnology all show a similar four-year decline – as if Biotechnology is fading from the popular imagination. At the same time, the trend for Biotech companies is significantly on the incline – even in these dark, dark economic times, which is sayin’ something — and the econo-pundits keep saying that drug-related biotech companies are havens from the storm or, even better, takeover targets by Big Pharma.
We’re not Real Big Thinkers here at Aminopop, but this generates a fair amount of cognitive dissonance for us.
Just Sayin’. What do you think? Discuss.
Posted: 24 Sep 2008 05:38 PM CDT
Noam Chomsky once said "If we do not believe in freedom of speech for those we despise we do not believe in it at all.". I couldn't agree more. See we have this tenured professor at Ottawa U who likes to stir shit, his name is Denis Rancourt. One day he decided to turn his environmental class into an activism class and decided to fight the powers or "speak truth to power" as he likes to say. He decided to get rid of the grading system and give A+ to everyone because grading maintains an oppressive class system that legitimizes the heredity of the rich elite. I personally would have been pissed if it had been my class and I was genuinely interested in learning about environmental chemistry, but certainly don't oppose those ideas being thought on his and his student's own time. He then practiced what is known as academic squatting (link to his blog) to show political documentaries and invite speakers and allow both students and the public to be exposed to those ideas in the university's space. Finally he put up a website whose sole purpose is to document anything that would be suspicious about the university called UofOwatch. In short he stirred shit.
Of course the university blew a fuse, he was stripped of teaching duties, cannot mentor graduate students, all the lawyers went after his UofOwatch site for libel and copyright infringement, and they tried to shut down his cinema night because it didn't include access for the deaf. See this is where the university failed to do the right thing. Yes he shouldn't be teaching activism in a chemistry class, yes it is inappropriate for him to have graduate students, because he doesn't do research but why make a martyr out of him. What's wrong with debating ideas and exposing students and the public with controversial political thoughts, what's wrong with criticizing the administration. If they had legitimized him instead, well he would've been largely ignored anyways, and the university could have taken the moral high ground. Instead we are at risk of losing academic freedom and the role of universities to promote free speech and discourse.
See that's the kicker, I don't agree with anything I've ever heard coming out of his mouth: I don't think global warming is a plot to keep the masses in fear, I don't think corporate interests control all academic research, I don't think chemotherapy has never been proven to work, I don't think tenure forces professors to turn into sheep, I don't think higher education stops us from thinking on our own, but goddamn it I do think he should be allowed to proclaim those ideas without being muzzled. Because if we don't let this professor criticize our university and expose his cockamamie ideas, then when somebody comes with something important to say we wont be able to hear them. So I appeal to you Mr. A-ROCK, someone I admire a great deal more than Denis, do the right thing. Remember the days when you organised peace conferences and brought Lennon to Canada, or when you came within a smidgen of passing the pot legalisation law as a justice minister? I want that guy back as my university president.
Posted: 24 Sep 2008 04:01 PM CDT
I’ve been meaning to write about recent two papers, one in Current Biology and one in Nature, that attempt to identify and characterize a relationship between genetic sequence or SNP and geography. Amazingly, both papers found a very strong correlation between genetics and geography.
From a news article regarding the paper in Nature (note that I haven’t verified that the paper supports the statement; HT: Yann Klimentidis’ Weblog):
Although there are some caveats, for example in one of the papers all of an individual’s grandparents had to have similar geographic origins in order for the method to identify ancestry, these types of studies will continue to discover and refine the methods and findings. As Kambiz stated at Anthropology.net, "With higher resolution GeneChips, ideally full genomes, and larger samples, we’ll be able see much more accurate genetic-geographic separations of populations."
There is also a short but very interesting video associated with the Nature paper (HT: ScienceRoll - you were right Berci!). From the video:
Posted: 24 Sep 2008 03:55 PM CDT
Posted: 24 Sep 2008 03:23 PM CDT
Amidst the current economic panic, I'm feeling more shocked than usual when listening to the flip-flopping, falsehoods, fabrications, backstepping, about-facing and unabashed spin-doctoring spewing forth from the news media. If watched long enough, one may even develop empathy for Henry Paulson who carries the weight of the global economy on his shoulders. Nevertheless, what do we know about making mistakes ? Not necessarily global financial catastrophies, but little everyday mistakes. Why do some of us learn from our mistakes ? What's going on in the brain ? Enter Michael Frank, Christopher D'Lauro and Tim Curran, in their paper entitled, "Cross-task individual differences in error processing: Neural, electrophysiological and genetic components" [Cognitive, Affective, & Behavioral Neuroscience (2007), 7 (4), 297-308]. Their paper provides some amazing insight into the workings of human error-processing.
It has been known for some time that when you make a mistakke - oops! - mistake, that there are various types of electrical current that emanate from the frontal midline (cingulate cortex) of your brain. The so-called error related negativity (ERN) occurs more strongly when you are more focused on being correct and also seems to be more strong in people with certain personality traits (apparently not news commentators or politicians) while the error positivity (Pe) occurs more strongly when you become consciously aware that you made an error (perhaps not functioning in news commentators or politicians). Perhaps the ERN and Pe are basic neural mechanisms that facilitate an organisms adaptive ability to stop and say, "hey, wait a minute, maybe I should try something new." The Frank et al., paper describes a relation between learning and dopamine levels, and suggests that when dopamine levels dip - as happens when our expectations are violated ("oh shit!, I bought stock in Lehman Brothers") - that this may facilitate the type of neural activity that causes us to stop and rethink things. To test whether dopamine might play a role in error processing, the team examined a common variant (rs4680) in the catechol-o-methyl transferase gene, a gene where A-carriers make a COMT enzyme that is slower to breakdown dopamine (a bulky methionine residue near the active site) than G-allele-carriers. Subjects performed a learning task where correct responses could be learned by either favoring positive feedback or avoiding negative feedback as compared to neutral stimuli. The team suspected that regardless of COMT genotype, however, there would be no COMT association with learning strategy, since COMT influences dopaminergic activity in the frontal cortex, and not in the striatum, which is the region that such reinforcement learning seems to be stored.
Interestingly, the team found that the error positivity (Pe) was higher in participants who were of the A/A genotype, but no difference in genetic groups for the error related negativity (ERN). This suggests that A/A subjects deploy more attentional focus when they realize they have made an error. Lucky folks ! My 23andMe profile shows a GG at this site, so it seems that when I make errors, I may have a normal ERN, but the subcortical dopamine that dips as a result does not (on average) result in much greater attentional focus. Oh well, I guess its the newsmedia pool for me.
Posted: 24 Sep 2008 12:44 PM CDT
The idea of writing this particular grant proposal at this specific time clearly makes no sense in the framework of my life, with teaching and traveling and kids and a million other things to do. It would border on the insane to try to do this now and to do it well. Yet the intrinsic impossibility of writing this proposal stays with me. It was with me in the pool this morning, where all was quiet except for the sound of strokes and flip turns in the water. It is with me now. I cannot resist think through some of our latest results.
And so it begins. Before I fully realize it, I am sucked into a whirlpool of ideas. I float on them, soon lost in the absolute freedom of thinking. I am absolutely engaged.
I am fascinated with something no one understands and only a few of us would care to. I am consumed with the desire to think through this mystery, to know it. As Thoreau said, "to gnaw at it, bury it, unearth it and gnaw at it still". It is exhilarating to be drawn into the deep realm of the undiscovered and it is a challenge to harness the wild power of scientific ideas by writing about them. I want to explain our research results clearly to my colleagues, propose a model and ask them "don't you see it too?" My intellect is engaged and my heart too, because I love this work.
I am oblivious to the looming demands of the 100 students that I will begin teaching tomorrow, deaf to the requests of colleagues to help out on this or that, rushed with my graduate students that need my advice, and indifferent to the calls of my husband for my attention. Yes, tonight, I will surely even be slow to respond to the hunger of my children.
"What?" I will say, looking up in a daze from the computer, "Dinnertime already?"
The scaffold of my day, the family schedule that brings a peaceful haven to our lives will be submerged in the pursuit of hypotheses and the design of experiments to test them.
So I adapt myself to the need to write. Oblivious to everything, as if time was ample, except for the pressing and peculiar desire to post this blog before I dive back in.
This post greatly benefited from Annie Dillard's wonderful book "The Writing Life"
Posted: 24 Sep 2008 12:29 PM CDT
Would you like to win a cash prize and maybe an expense paid trip to New York City?
Winners (2 from each grade) will receive cash awards, from $500 to $2,500, and an all-expense paid trip to New York City to attend the awards ceremony at the Museum.
The contest involves investigating questions in ecology, biology, Earth science and astronomy and writing an essay. More information can be found here.Read the comments on this post...
Posted: 24 Sep 2008 12:24 PM CDT
I'm happy to be hosting the 50th edition of the Four Stone Hearth Anthropology Blog Carnival!
We've got a wide array of Anthropology topics. I'll go from social/cultural anthropology, then into archaeology, and then into biological anthropology.
Daniel at Neuroanthropology shares with us Alesha Sivartha's collection of drawings representing the domains of life and culture that brains might be devoted to dealing with. This is interesting in the sense that evolutionary psychologists have argued that the brain is not like a general purpose computer, but rather like a Swiss army knife with domain specific mechanisms evolved to deal with specific problems such as face recognition, social relationships, mental maps, etc..
Daniel has another interesting post about Race in the Race for President of the US, which reminds us that racial dynamics are never far from the lived experience of Americans.
Magnus Reuterdahl at Testimony at the Spade discusses Mark Twain's visit to Jonkoping, Sweden.
Terry Toohill, guest blogger at Remote Central, discusses the evidence and misconceptions surrounding the processes of evolution, and might I add, provides plenty of references.
Martin at Aardvarchaeology shares his experience with the trials and tribulations of archaeological digs in Sweden.
At the Southeast Asian Archaeology Newblog, we see that six new Neolithic burials from Sarawak from the Niah cave complex have been recently put on display.
"More significantly, the skeletons are of the Australomelanasoid affinity, which means they were natives of Sundaland (the geological land shelf on which much of island Southeast Asia sits on) and possibly represent the continuous habitation of the cave site rather part of the migratory group originating from Southern China that is thought to populate Southeast Asia in this period" (from 2-3 thousand years ago)The past couple of weeks has seen several stories about Neanderthals.
As usual, John Hawks has a wealth of information and insight:
Afarensis also discusses a paper about Neanderthal brain size and maturation which argues that Neanderthals grew quickly but matured later than modern humans, suggesting that their overall life history was perhaps slower paced than that of modern humans. Afarensis also discusses the use of marine food resources by Neanderthals, before the most recent piece of evidence came out in PNAS.
Dienekes has his usual dizzying array of posts from a wide variety of topics in evolutionary and molecular anthropology.
I'll just point out the post on Stonehenge and how it has been dated more accurately, and how it has been suggested that it was a healing center.
Razib at GNXP has a great post on a recent NYT article about David Goldstein on the HapMap, selection and race. Many other bloggers (John Hawks, Genetic Future etc...) have also commented on this article. In this article David Goldstein questions the efficiency of the process by which we currently look for the genetic basis for disease (and intelligence).
Finally, let me point you to Kambiz's always excellent and thorough Anthropology.net blog. He has recently posted about a new study published in PLoS Genetics that examines how genes involved in the immune system can predict human mating patterns.
Posted: 24 Sep 2008 10:32 AM CDT
Genetic testing is a very powerful tool. Done properly with the right counseling, it can mean healthier and prolonged lives for many patients. For example, variations in the BRCA gene are a predictor for breast and ovarian cancer. Men and women with a family history of breast and ovarian cancer often want to get tested for this variant. If they test positive, many will alter their behavior, like quiting smoking or halting the use of birth control pills. Some will even under go prophylactic surgery removing breast and ovarian tissue to prevent the development of cancer.
Usually these patients are consenting adults who are over 25. They can understand the implications and act appropriately. But what if a parent tests positive for a inherited predictive gene and wants to test their child? Is 18 old enough? What about 16? Would it shock you to know that some parents test their children for cancer predicting genes as young as 4?
The AP has a great piece on the implications of testing children too early. What is too early? It depends on the clinical relevance of the particular test. If those who have the BRCA variant rarely develop cancer before the age of 25, then what would be the point of genetic testing for a 4 year-old? If there is nothing that is to be done until the child is older why burden them the information?
Here are some reasons given to test a child:
Yes, information is a good thing. But can't the parents of these children warn them about risky behavior without getting the test done? Then the child can choose for themselves if they want the genetic information or not. My father warned me that his side of the family had a history of alcoholism. I didn't need a genetic test to avoid heavy drinking.
The major concerns with testing children are the ethical and emotional implications. Can a child really give informed consent and is the information too much for them too handle?:
So the American Society of Clinical Oncology and other groups say that when the risk of childhood cancer is low and nothing can be done to lower it, children should not be given gene tests.
Hear hear! And this is why I agree:
Genetics is rarely 100% predictive but in this age where science is king, children and young adults may feel that they have been handed a genetic death sentence. This may also effect their plans for children and family:
If you or someone you know decides to test their children for cancer or other predictive genetic tests, all I can say is counseling is critical. Do not take the test results, stick them in a drawer and then live in guilt and fear. Take them to a genetic counselor and get informed!
Hat Tip: Bioethics.com
Posted: 24 Sep 2008 10:18 AM CDT
If you like cool and unusual photos be sure to take a look at the 2008 Nikon Small World competition site. You can view lots of lovely pictures of things found under a microscope and vote for your favorite ones. You don't even have to focus the microscope!
One of my favorites is the tubeworm larva. It looks something from outer space.
There's even a contest to identify some of the more unconventional images. I only got three out of five. ;-(
You can find them at www.nikonsmallworld.comRead the comments on this post...
Posted: 24 Sep 2008 08:43 AM CDT
Part IV. Assembling the details and making the case for a novel paramyxovirus
This is the fourth in a five part series on an unexpected discovery of a paramyxovirus in a mosquito. In this part, we take a look at all the evidence we can find and try to figure out how a gene from a virus came to be part of the Aedes aegypti genome.
image from the Public Health Library
I. The back story from the genome record
Posted: 24 Sep 2008 07:58 AM CDT
Some new IA posts for those who dabble in reading not just science geek blogs (bayblab) but IT geek blogs aswell. Broaden your geekness! Lots of stuff on digital privacy and free speech and the usual collection of 'Fun Stuff' including a Swedish Funiture Name Generator.
Posted: 24 Sep 2008 07:15 AM CDT
Jove is featuring a movie which explains how to study the coordination of membrane biogenesis by a luciferase-based reporter gene approach using the Dual-Glo Luciferase Assay System from Promega. As usual, Jove provides a step-by-step protocol that can be commented for asking clarifications.
In my humble opinion, this is definitively the new revolutionary way to make science and I'm quite surprised to get replies from big seniors wondering only about Jove's impact factor.
Shaochong Zhang, Axel Nohturfft (2008). Studying Membrane Biogenesis with a Luciferase-Based Reporter Gene Assay Journal of Visualized Experiments
Posted: 24 Sep 2008 07:00 AM CDT
This week in my SpectroscopyNOW column, I have four new posts covering, as usual, a wide range of solutions to scientific and technical problems. First up, is the discovery that compounds found in cannabis could lead to novel antibiotics that are less susceptible to resistance than conventional drugs. Then, we have a new type of spectroscopy that allows scientists to carry out broadband analysis of artificial atoms held at temperatures close to absolute zero. Next, is word from chemists that they have developed a new type of reaction flask that can carry out reactions in the solid state. Finally, this week, we hear of testing times for biomass, where modern spectral analysis could help in the processing of old, treated wood as a renewable fuel resource.
Doping the superbugs - Substances found in cannabis could be used to fight potentially lethal superbugs, such as antibiotic-resistant bacteria, without the mood-altering effects, according to researchers in Italy and the UK. Cannabis sativa (L. Cannabinaceae) extracts may also provide an alternative to synthetic antibacterial substances used in personal hygiene products, including hand wash and cosmetics.
Diamond amp - A new spectroscopic approach to measuring the energy levels of an atomic system has been developed by US researchers. Amplitude spectroscopy can be used to measure the energies of certain natural and artificial atoms and molecules over extremely broad bandwidth by scanning the amplitude of the applied radiation rather than its frequency. The new technique allows the characterization of multiple energy levels in the system, and so overcomes a key challenge to realization of powerful quantum computers. It is applicable to systems with strong coupling to external fields, including artificial atoms, spin systems, cold atoms and molecules, and molecular magnets.
Littlest test-tube - Chemists in Japan have synthesized a new porous material that acts as a microscopic solid-state reaction vessel. Chemical changes taking place in each pore can be tracked using X-ray crystallography the team explains.
Testing times for biomass - Spectroscopy can be used to determine the amount of ash and char present in various types of biomass derived from wood, according to researchers in Japan and the US. Their analytical approach could help in the development of renewable resources for fuels to replace fossil fuels.
Posted: 24 Sep 2008 01:40 AM CDT
Well, it mainly concerns eradicating infectious diseases with smallpox given as an example.
In case you’ve forgotten, smallpox was eradicated in the late 1970s (last case in 1977) through a vaccination program. My parents received the vaccine but with the last case in Denmark in 1970 I didn’t (I was born in 1975).
It is a bit cool to think about it. A disease was important enough to cause a global vaccination program in my parents generation, but for me there was no point; the disease had been wiped out. I was vaccinated against TB (Calmette vaccination) but my younger sister weren’t ’cause by that time there were so few cases in Denmark that it wasn’t worth it.
We are getting pretty good at this.
Now, in the Google blog post, Dr. Larry Brilliant compares smallpox to the Black Death and bird flu. That is a bit dramatic, I think. Well, maybe not the bird flu — we don’t know how deadly that will be — but the Black Death was a bit more deadly. Maybe not in the long run — smallpox has killed its share of people — but in the short run a pandemic like the Black Death (and more so the Spanish flu) is a lot more worrying.
To identify potentially emerging epidemics, Larry mentions Google’s Predict and Prevent initiative.
The post is a bit short on visions, at least compared to the earlier Google at 10 posts.
Epidemics (and pandemics) is an important issue, and something like Predict and Prevent can be important. But what will it do in the future? What are the visions?
Posted: 23 Sep 2008 09:28 PM CDT
Some good new articles in PLoS Biology in the last few weeks worth checking out. There is definitely a theme there if you want to look for it. So here are some of the papers connected to that theme and even one that covers both.
Posted: 23 Sep 2008 08:00 PM CDT
Of course that isn't exactly what the governor of Wisconsin said, but that is what he meant. This article from the Badger-Herald sports the headline, "Doyle: Science over religion, politics." And Gov. Doyle is quoted as saying:
And he asks:
Doyle's answer would be a resounding "Yes!"
So let us take a closer look at what Doyle is really saying. "Religion, politics, and personal ideolgies" is really just inflammatory language. There are people of all religions that support embryonic stem cell research and atheists who do not. There are Republicans that support embryonic stem cell research and Democrats who do not. And there are lots of people with "personal ideolgies" that think embryo-destructive research is fine. Doyle is one of them.
What Doyle is really saying is that science should trump any "religion, politics, and personal ideolgies" that dare to limit therapeutic cloning and embryonic stem cell research. Doyle thinks science should not be detered by those who have qualms about the ethics of the research. He believes science should only be held accountable to those who want it to go forward regardless of how many human embryos are created or destroyed.
Because science has no internal way to decide on ethical issues, it needs philosophy, history, theology and the law to be it's moral compass. Nothing is quite as scary to me than the idea of science with no ethical constraints. Science without guidance from such scientifically distasteful things as "religion, politics, and personal ideolgies" is a horror I never want to witness.
So what Doyle means when he says he wants science over "religion, politics, and personal ideolgies" is that he wants science over ethical restraints. Science over ethics.
No thank-you Governor Doyle.
Posted: 23 Sep 2008 12:01 PM CDT
This November, Michigan is voting on Prop 2. which would allow for the destruction of embryos for research. A new "study" convienently released says that voting for Prop 2 would, among other things, save the state $80 million dollars and provide relief for 770,000 Michigan residents. From the Traverse City Record-Eagle:
Those are some pretty big IFs. I am seriously wondering how anyone to come up with a study that speculates about anything regarding the impact of embryonic stem cell research. Embryonic stem cell treatments for patients don't even exist yet! This "study" sounds like smoke and mirrors to me. But I am not the only one:
But critics like Michael Craw, a political science professor at Michigan State University, challenge those findings.
Even the author, Goodman said his numbers are questionable:
Goodman acknowledged critics may take issue with the estimates and that the economic gains could be smaller than predicted. Asked about the 1 percent figure, Goodman acknowledged it was somewhat "arbitrary."
I suggest the Michigan Citizens for Embryonic Stem Cell Research (MCSCR) "praise" a better study if there is one. And that maybe the point. If this is the best "study" forthcoming on the "benefits" of embryonic stem cell research, then that is pretty pathetic. Let us hope Michigan residents aren't fooled.
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